Brett, I haven't poked into your code or the plugin activation code in WP, but guessing off the top of my head, I wonder if it has anything to do with the fact that the plugin directory has a hyphen in it while the main PHP file within the directory does not?

I did find the solution to this, it was because the copy of PHP Markdown Extra I include had a second WordPress plugin inside it which was being read at the time of install. Current versions should not suffer from this issue.